The pipes carrying our drinking water also house microbes with great potential to impact public health. | Flickr/uncoolbob

Despite our love for hand sanitizer and antibacterial cleaning products, we humans spend our days immersed in microbes, even when we are indoors, sealed away from much of the natural world.

For the most part, cultivating a diverse assortment of microbes in the environments we build is better for human health than trying to eradicate them, experts said at related AAAS events on 26-27 March. An understanding of what makes for a healthy "microbiome" is just getting off the ground, they agreed, thanks in large part to next-generation DNA-sequencing technology that can quickly identify microbes' genetic signatures.

100 Trillion

The approximate number of microbes in the human body

Mark Hernandez | AAAS/Kathy Wren

At a day-long symposium at AAAS headquarters, which was organized by AAAS in collaboration with the Alfred P. Sloan Foundation, several expert panels discussed microbiomes in a range of built environments, from the International Space Station to green buildings. Three of the speakers also participated in a briefing on Capitol Hill the day before, where they emphasized the need for better integration between the fields of microbiology and civil engineering.

Mark Hernandez, a professor in the Department of Civil, Environmental, and Architectural Engineering at the University of Colorado, described himself and his colleagues as "probably the first generation of civil engineers that have a strong microbiological training. Not too long ago, that didn't happen," he said. "Things were black boxed. Although we were designing chlorination systems, we weren't really trained in the fundamentals of microbiology."

Bacteria, viruses and other single-celled creatures spread surprisingly quickly through the environment, aided and abetted by people, who each carry their own unique assortment of microbes, according to Jack Gilbert, an environmental microbiologist with Argonne National Laboratories and the University of Chicago, who also spoke at the Hill briefing. He described studies from his laboratory showing that within hours after a person enters an indoor space, their own microbial signature begins to appear on surfaces in the area.

In general, being surrounded by a diverse microbiome is a good thing. Gilbert's team has also placed microbe-sampling devices on streetlights across Chicago, with the aim of helping to develop urban areas whose microbes show "more rich biodiversity all around, thereby increasing the microbial health of those spaces," he said. However, some microbe species can be harmful, including some that live in places where their presence isn't yet widely recognized.

Jack Gilbert | AAAS/Kathy Wren

A rendering of sensing devices that sample air-borne microbes. | Courtesy of the Art Institute of Chicago

The pipes carrying our drinking water and sewage are home to microbes with great potential to impact public health. These aging systems are prone to leaks and desperately in need of replacement throughout much of the United States. In its 2013 Report Card for America's Infrastructure, the American Society of Civil Engineers has assigned a grade of D to the country's wastewater and drinking water infrastructure.

Amy Pruden, a professor of civil and environmental engineering at Virginia Tech, hopes the recommendations from reports like this one may also offer an opportunity to address another urgent issue: the buildup of antibiotic resistance in bacteria. According to a 2013 report from the Centers for Disease Control and Prevention, 2 million Americans fall ill from antibiotic-resistant bacteria each year, and at least 23,000 die as a direct result of these infections.

"Our drinking water is not sterile. It is a rich, microbial habitat. I argue that we need to accept this to move the field of water engineering forward."

Amy Pruden, Virginia Tech

Amy Pruden | AAAS/Kathy Wren

Sampling for microbial DNA in the Poudre River. | Courtesy of Emily Lipscomb

10,000 Cells

The average number of microbes in a milliliter of tap water

Antibiotic-resistant microbes typically live in the guts of humans and livestock, and thus in our wastewater, but even if they are killed in waste-treatment plants, their DNA can still travel into our waterways. Analyzing the DNA in water samples from the Poudre River watershed in northern Colorado, Pruden and her colleagues have discovered antibiotic resistance genes in a troubling pattern.

"We saw a relationship that astounded us, especially in such a complex watershed. We saw a near-perfect correlation" between the levels of antibiotic resistance genes and the numbers and sizes of upstream wastewater treatment plants and livestock operations, said Pruden.

Could water treatment systems be upgraded to remove or damage DNA? More research will be necessary to tackle this problem and learn more about the makeup of the water microbiome, which may have additional impacts on human health. For example, some disease-causing bacteria, such as Legionella pneumophila and Pseudomonas aeruginosa are now the primary source of waterborne disease outbreaks in the United States. Maintaining a diverse community of other waterborne microbes is probably the most realistic way to keep these harmful agents in check, according to Pruden.

"Our drinking water is not sterile. It is a rich, microbial habitat. I argue that we need to accept this to move the field of water engineering forward," she said.

The situation is different, though no less urgent, with wastewater, which flows through sewers that are corroding rapidly. Microbes on the sewer ceilings oxidize hydrogen sulfide gas from the sludge below, producing sulfuric acid that eats away at the concrete and drastically shortens the pipes' lifespan. Hernandez cited estimates from the American Society of Civil Engineers and the Environmental Protection Agency that place the cost of replacing these pipes and making other updates to the U.S. wastewater infrastructure at roughly $3 $300 billion over the next 20 years.

While it's well known that sewer sludge teems with a rich array of microbes, Hernandez and his colleagues have determined using DNA sequencing that the communities along the sewer ceilings consist of just a handful of species. In theory, this low level of diversity may make it possible to kill off these harmful bacteria without causing collateral damage to the rest of the sewer microbiome below. In the meantime, Hernandez and his colleagues are also experimenting with ways to embed concrete with tiny, metal-carbon clumps or other substances that may inhibit bacterial growth.

Experiments on concrete corrosion. The untreated block in the lower right corner is the most corroded.| Courtesy of Mark Hernandez

The same type of sequencing technology is also at the heart of Gilbert's efforts to understand how microbes spread through rooms and buildings. He and his colleagues had an unusual opportunity to collect and analyze microbe samples throughout a newly built Chicago hospital, before and after it opened. Overall microbial diversity increased noticeably within days after the hospital's opening and was even greater on bedrails, floors and other inanimate surfaces than it was on people's skin. The team has continued to take millions of samples to build an "epic database" of the microbial variation throughout the hospital, he said.

This information might be useful for matching patients up with hospital beds or rooms based on who has occupied the room previously and which infections the new patients may be especially vulnerable to. Ultimately, patients' unique microbial profiles may even become part of their medical records, Gilbert proposed.